Comparison of next generation sequencing-based and methylated DNA immunoprecipitation-based approaches for fetal aneuploidy non-invasive prenatal testing

Over the past few years, many researchers have attempted to develop non-invasive prenatal testing methods in order to investigate the genetic status of the fetus. The aim is to avoid invasive procedures such as chorionic villus and amniotic fluid sampling, which result in a significant risk for pregnancy loss. The discovery of cell free fetal DNA circulating in the maternal blood has great potential for the development of non-invasive prenatal testing (NIPT) methodologies. Such strategies have been successfully applied for the determination of the fetal rhesus status and inherited monogenic disease but the field of fetal aneuploidy investigation seems to be more challenging. The main reason for this is that the maternal cell free DNA in the mother’s plasma is far more abundant, and because it is identical to half of the corresponding fetal DNA. Approaches developed are mainly based on next generation sequencing (NGS) technologies and epigenetic genetic modifications, such as fetal-maternal DNA differential methylation. At present, genetic services for non-invasive fetal aneuploidy detection are offered using NGS-based approaches but, for reasons that are presented herein, they still serve as screening tests which are not readily accessed by the majority of couples. Here we discuss the limitations of both strategies for NIPT and the future potential of the methods developed.

Osteopathia striata with cranial sclerosis, Wilms’ tumor and the WTX gene

Osteopathia striata with cranial sclerosis (OSCS, OMIM#300373) is an X-linked dominant sclerosing bone dysplasia that shows a distinct phenotype in females and males. In 2009, Zandra Jenkins et al found that germline mutations in the FAM123B/WTX/AMER1 gene, mapped to chromosome Xq11.2, cause both the familial and sporadic forms of OSCS. Intriguingly, the WTX gene was already known as a putative tumor suppressor gene, since in 2007 Rivera et al had reported inactivating WTX mutations in Wilms’ tumor (WT), the most frequent renal tumor of childhood. Here we review the heterogeneous clinical presentation of OSCS patients and the involvement of WTX anomalies in OSCS and in WT.

Regulation of the cell fate by DNA damage and hypoxia

In order to provide the means for the design of novel rational anti-cancer drug therapies research efforts are concentrated on unravelling the molecular circuits which induce programmed cell death and block proliferation of cancer cells. Modern therapeutic strategies are based on the understanding of the complexity of physiological functions such as differentiation, development, immune responses, cell-cycle arrest, DNA damage repair, apoptosis, autophagy, energy metabolism, and senescence. It has become evident that this knowledge will provide the means to target the components of the pathways involved in these processes in a specific and selective manner thus paving the way for the development of effective and personalised anti-cancer therapies. Transcription is a crucial cellular process that regulates a multitude of physiological functions, which are essential in disease progression and cellular response to therapy. Transcription factors such as the p53 tumor suppressor and the hypoxia-inducible factor-α (HIF-α) are key players in carcinogenesis and cellular response to cancer therapies. Both of these transcription factors regulate gene expression of genes involved in cell death and proliferation, in some cases cooperating towards producing the same outcome and in some others mediating opposing effects. It is thus apparent that fine tuning of the activity of these transcription factors is essential to determine the cellular response to therapeutic regimens, in other words whether tumor cells will commit to apoptosis or evade engagement with the anti-proliferative effects of drugs leading to drug resistance. Our observations support the notion that the functional crosstalk between HIF-1α and p53 pathways and thus the fine tuning of their transcriptional activity is mediated by cofactors shared between the two transcription factors such as components of the p300 co-activator multiprotein complex. In particular, there is evidence to suggest that differential composition of the co-modulatory protein complexes associated with p53 and HIF-1α under diverse types of stress conditions differentially regulate the expression of distinct subsets of p53 and HIF-1α target genes involved in processes such as cell cycle arrest, apoptosis, chronic inflammation, and cellular energy metabolism thereby determining the cellular fate under particular types of micro-environmental stress.

Earlier onset and multiple primaries in familial as opposed to sporadic esophageal cancer

AIM: To study the differences in onset age and multiple primary cancers between familial and sporadic esophageal squamous cell carcinoma (ESCC).

METHODS: The differences in onset age and multiple primary cancers were analyzed between ESCC patients with (n = 766) and without (n = 1776) a family history of the cancer. The cases analyzed constituted all consecutive patients who had undergone cure-intent surgery at the Department of Thoracic Surgery of the 4^th Hospital of Hebei Medical University from January 1 1975 to December 31 1989. Because we also originally aimed to examine the difference in survival time, only older subjects with a long follow-up period were selected.

RESULTS: Overall, patients with ESCC and a positive family history of the cancer had a significantly younger age at onset and more multiple primary cancers than those without a positive family history (51.83 ± 8.39 vs 53.49 ± 8.23 years old, P = 0.000; 5.50% vs 1.70%, P = 0.000). Both of these differences were evident in subgroup analyses, however, no correlations were observed. While age at onset differed significantly by family history in males, smokers, and drinkers, the difference in multiple primary cancers by family history was significant in nonsmoking, nondrinking, and younger onset patients. In multivariate analysis, age over 50 years, tobacco smoking, and multiple primary cancers were found to be significant predictors of familial cancer: the corresponding OR (95%CI) and P-value were 0.974 (0.963-0.985) and 0.000; 1.271 (1.053-1.535) and 0.012; and 4.265 (2.535-7.176) and 0.000, respectively.

CONCLUSION: Patients with ESCC and a positive family history of the cancer had a significantly younger onset age and more multiple primary cancers than those without a positive family history. Sub-group analyses indicated that younger onset age may be due to the interaction of genetic predisposition and environmental hazards, and multiple primary cancers may only be due to genetic predisposition.

Genomic microarrays in prenatal diagnosis

The application of microarray-based techniques for the diagnosis of genomic rearrangements has been steadily growing in popularity since its introduction in 2004. Given the many advantages of these techniques over conventional cytogenetics, there is increasing pressure towards their application in prenatal diagnosis. However, there remain several important issues that must be addressed. For example, microarray-based techniques (comparative genomic hybridization-based arrays and single nucleotide polymorphism-based arrays) allow detection of even very small genomic imbalances that can determine pathological clinical conditions. In addition, there are other copy number variations which represent normal variation, with no detectable effects on phenotype. Given the still incomplete knowledge of the changes in our genome and the associated phenotypes, microarray-based diagnosis is likely to find variants of uncertain and unknown clinical significance. The interpretation of these variants is now a major challenge for the medical geneticist, who often find it difficult to establish precise correlations between genotype and phenotype. There is sufficient available evidence to justify the use of microarray-based diagnostics for a select number of specific conditions, but there is also an inevitable trend towards ever wider application. It is very important that this drift does not progress in an unchecked and uncontrolled manner under the thrust of commercial interests. Therefore, we recommend that scientific societies be vigilant and take an advisory role in the adopting of these technologies as new scientific knowledge becomes available.

Evolving ethical issues in third party reproduction: Local and global considerations

There continues to be an increase in utilization of assisted reproductive technology (ART), including the use of third party gametes. Specifically, the use of third party oocytes, most recently reported in 2010 by the United States (US) Center for Disease Control and Society of Reproductive Medicine, accounted for 15 504 cycles and 7334 live births. This translates into approximately 11% of all the in vitro fertilization cases performed in the US. As utilization increases and the technological tools advance, they have created underappreciated and unforeseen ethical quandaries. As such, many practitioners think they “have heard it all”. However, each ART scenario is novel with the potential to pose complex unforeseen issues, potentially creating global challenges that could impact broad social and legal questions and test the moral consciousness’ of practitioners, policymakers and patients. While there are published US national guidelines to assist practitioners, we have identified new complex issues in assisted reproduction that present unique challenges, and we give a perspective from our eyes in the Western Hemisphere looking out to a global level. Specifically, this review focuses on some of the more recent and evolving issues that currently are and will be confronting us in the upcoming years. Particular attention focuses on discrepancies between third party legal contracts and ART consents regarding level of information sharing, and oocyte and embryo directives and management; dilemmas and obligations surrounding disclosure of medical outcomes especially in the context of growing access to Direct to Consumer genetic testing and Reproductive Tourism-Exile. Given the complexity of these and other ethical questions, finding answers may be achieved by ending the isolation of reproductive professionals and instead promoting increased and consistent communication among physicians, embryologists, therapists and reproductive attorneys to confront these evolving ethical quandaries.

Malignant pheochromocytoma in neurofibromatosis; mutation screening of RET proto-oncogene, VHL and SDH gene

AIM: To investigate pathogenic mutations related to malignant pheochromocytoma in neurofibromatosis (NF).

METHODS: We present a patient with NF and metastatic pheochromocytoma in whom genetic screening for presence of pathogenic mutations in RET proto-oncogene, von Hippel-Lindau (VHL) and succinate dehydrogenase complex subunits B (SDHB) genes were investigated. RET proto-oncogene mutation screening for exons 10, 11, 13, 14, 15, 16 were examined by polymerase chain reaction (PCR) and direct DNA sequencing in patient. Mutation screening for exons 1, 2, 3 of VHL gene was carried out. Both forward and reverse strands were subjected to direct sequencing after PCR amplification. The entire coding sequence of SDHB gene was screened for the presence of pathogenic mutations by PCR-sequencing.

RESULTS: A 45-year-old man presented with abdominal pain and hypertension over the previous year. The patient was a known case of neurofibromatosis type 1 (NF1) who presented at the age of 15 years with hyperpigmented and hypopigmented lesions. After complete evaluation for hypertension, biochemical tests and imagings indicated a malignant pheochromocytoma of 120 mm × 70 mm in size. The patient underwent left adrenalectomy, nephrectomy and splenectomy. After surgery the symptoms improved and blood pressure was controlled. After 5 years he was admitted again for evaluation of hypertensive crisis. Biochemical tests were again consistent with pheochromocytoma and disease relapse. Imaging studies and liver biopsy confirmed metastatic pheochromocytoma to the liver and para-aortic area. 131 Iodine-metaiodobenzylguanidine therapy was carried out. Genetic screening of VHL (exons 1, 2, 3), RET proto-oncogene (exons 10, 11, 13, 14, 15, 16) and SDH complex subunits revealed no pathogenic mutation.

CONCLUSION: We conclude that mutations in the NF1 gene are responsible for the patient’s clinical findings. However, would be helpful to further examine somatic mutations for a more precise study of genotype-phenotype correlation.

Clinical utilities and end-user experience of pharmacogenomics: 39 mo of clinical implementation experience in an Australian hospital setting

BACKGROUND

Pharmacogenomics (PG) testing is under-utilised in Australia. Our research provides Australia-specific data on the perspectives of patients who have had PG testing and those of the clinicians involved in their care, with the aim to inform wider adoption of PG into routine clinical practice.

AIM

To investigate the frequency of actionable drug gene interactions and assess the perceived utility of PG among patients and clinicians.

METHODS

We conducted a retrospective audit of PG undertaken by 100 patients at an Australian public hospital genetics service from 2018 to 2021. Via electronic surveys we compared and contrasted the experience, understanding and usage of results between these patients and their clinicians.

RESULTS

Of 100 patients who had PG, 84% were taking prescription medications, of which 67% were taking medications with actionable drug-gene interactions. Twenty-five out of 81 invited patients and 17 out of 89 invited clinicians completed the surveys. Sixty-eight percent of patients understood their PG results and 48% had medications changed following testing. Paired patient-clinician surveys showed patient-perceived utility and experience was positive, contrasting their clinicians’ hesitancy on PG adoption who identified insufficient education/training, lack of clinical support, test turnaround time and cost as barriers to adoption.

CONCLUSION

Our dichotomous findings between the perspectives of our patient and clinician cohorts suggest the uptake of PG is likely to be driven by patients and clinicians need to be prepared to provide information and guidance to their patients.

Phenotypic and cytogenetic features of an Iranian child with tetrasomy 18p syndrome: A case report

BACKGROUND

Tetrasomy 18p is a rare chromosome abnormality disorder known to have considerable variability in clinical features and gathering data from different cases will help clinicians and researchers learn about its genotype-phenotype relationship and diagnosis.

CASE SUMMARY

Herein, we have reviewed the literature on phenotypic features of this disorder and described the phenotypic and cytogenetic features of a girl of early childhood with tetrasomy 18p for the first time from Iran. This patient showed a strong sense of smell (a unique feature not reported previously for this syndrome), had clenched hand, pes planus, forward head posture in walking and hirsutism (dysmorphic features less reported), and showed 10 clinical features that are generally observed in previously reported cases, including developmental delay/intellectual disability, triangular face, smooth philtrum, feeding difficulties, hypotonia, epicanthus, strabismus, history of constipation, growth retardation and foot anomalies. G-banding chromosome analysis from peripheral blood revealed an abnormal female karyotype with a small marker chromosome (47,XX, +mar), and oligo-array comparative genomic hybridization displayed a gain of 14Mb of the 18p arm containing 56 Online Mendelian Inheritance in Man (OMIM) genes in this patient. Overall, this patient seems to have mild phenotypes.

CONCLUSION

This Iranian tetrasomy 18p child displays a uniquely strong sense of smell, some less reported dysmorphic features and ten features generally reported.

Genome-wide associations, polygenic risk, and Mendelian randomization reveal limited interactions between John Henryism and cynicism

BACKGROUND

John Henryism (JH) is a strategy for dealing with chronic psychological stress characterized by high levels of physical effort and work. Cynicism is a belief that people are motivated primarily by self-interest. High scores on the JH scale and cynicism measures correlate with an increased risk of cardiovascular disease. High cynicism is also a hallmark of burnout syndrome, another known risk factor for heart disease.

AIM

To evaluate possible interactions between JH and cynicism hoping to clarify risk factors of burnout.

METHODS

We analyzed genetic and psychological data available from the Database of Genotypes and Phenotypes for genome-wide associations with these traits. We split the total available samples and used plink to perform the association studies on the discovery set (n = 1852, 80%) and tested for replication using the validation set (n = 465). We used scikit-learn to perform supervised machine learning for developing genetic risk algorithms.

RESULTS

We identified 2, 727, and 204 genetic associations for scores on the JH, cynicism and cynical distrust (CD) scales, respectively. We also found 173 associations with high cynicism, 109 with high CD, but no associations with high JH. We also produced polygenic classifiers for high cynicism using machine learning with areas under the receiver operator characteristics curve greater than 0.7.

CONCLUSION

We found significant genetic components to these traits but no evidence of an interaction. Therefore, while there may be a genetic risk, JH is not likely a burnout risk factor.

Role of IL-2/IL-2 receptor in pathogenesis of autoimmune disorders: Genetic and therapeutic aspects

Interleukin-2 (IL-2) is an important cytokine that plays a key role in the immune response. The IL-2 receptor (IL-2R) is composed of three subunits, alpha, beta, and gamma, with the alpha subunit having the highest affinity for IL-2. Several studies reported that immune dysregulation of IL-2 may cause tissue injury as well as damage leading to the pathogenesis of various autoimmune diseases such as acute necrotizing vasculitis in systemic lupus erythematosus (SLE), inflammatory synovitis in rheumatoid arthritis (RA), salivary and lacrimal gland dys-function in Sjogren syndrome (SS), obliterative vasculopathy fibrosis in systemic sclerosis (SSc), and inflammatory demyelination in multiple sclerosis (MS). The aim of this review paper was to examine the role of IL-2/IL-2R in various autoimmune disorders, taking into account recent advancements and discoveries, gaps in the current literature, ongoing debates, and potential avenues for future research. The focus of this review is on systemic lupus erythematosus, rheumatoid arthritis, systemic sclerosis, sjogren syndrome, and multiple sclerosis, which are all linked to the malfunctioning of IL-2/IL-2R. In genetic studies, gene polymorphisms of IL-2 such as IL-2 330/T, IL-2 330/G, and rs2069763 are involved in increasing the risk of SLE. Furthermore, genetic associations of IL-2/IL-2R such as rs791588, rs2281089, rs2104286, rs11594656, and rs35285258 are significantly associated with RA susceptibility. The IL-2 polymorphism including rs2069762A, rs6822844T, rs6835457G, and rs907715T are significant connections with systemic sclerosis. In addition, rs2104286 (IL-2), rs11594656 (IL-2RA), rs35285258 (IL-2RB) gene polymorphism significant increases the risk of multiple sclerosis. In therapeutic approaches, low-dose IL-2 therapy could regulate Tfr and Tfh cells, resulting in a reduction in disease activity in the SLE patients. In addition, elevated sIL-2R levels in the peripheral blood of SLE patients could be linked to an immunoregulatory imbalance, which may contribute to the onset and progression of SLE. Consequently, sIL-2R could potentially be a target for future SLE therapy. Moreover, Low dose-IL2 was well-tolerated, and low levels of Treg and high levels of IL-21 were associated with positive responses to Ld-IL2 suggested to be a safe and effective treatment for RA. Additionally, low-dose IL-2 treatment improves the exocrine glands' ability to secrete saliva in SS-affected mice. Whereas, Basiliximab targets the alpha chain of the IL-2 receptor suggested as a potential treatment for SSc. Also, pre-and post-treatment with Tregs, MDSCs, and IL-2 may have the potential to prevent EAE induction in patients with MS. It is suggested that further studies should be conducted on IL-2 polymorphism in Sjogren syndrome.

Overlap of genetic influences in phenotypes classically categorized as psychiatric vs medical disorders

Psychiatric disorders have traditionally been segregated from medical disorders in terms of drugs, treatment, insurance coverage and training of clinicians. This segregation is consistent with the long-standing observation that there are inherent differences between psychiatric disorders (diseases relating to thoughts, feelings and behavior) and medical disorders (diseases relating to physical processes). However, these differences are growing less distinct as we improve our understanding of the roles of epistasis and pleiotropy in medical genetics. Both psychiatric and medical disorders are predisposed in part by genetic variation, and psychiatric disorders tend to be comorbid with medical disorders. One hypothesis on this interaction posits that certain combinations of genetic variants (epistasis) influence psychiatric disorders due to their impact on the brain, but the associated genes are also expressed in other tissues so the same groups of variants influence medical disorders (pleiotropy). The observation that psychiatric and medical disorders may interact is not novel. Equally, both epistasis and pleiotropy are fundamental concepts in medical genetics. However, we are just beginning to understand how genetic variation can influence both psychiatric and medical disorders. In our recent work, we have discovered gene networks significantly associated with psychiatric and substance use disorders. Invariably, these networks are also significantly associated with medical disorders. Recognizing how genetic variation can influence both psychiatric and medical disorders will help us to understand the etiology of the individual and comorbid disease phenotypes, predict and minimize side effects in drug and other treatments, and help to reduce stigma associated with psychiatric disorders.

Acquisition and dissemination mechanisms of CTXΦ in Vibrio cholerae: New paradigm for dif residents

Vibrio cholerae (V. cholerae) genome is equipped with a number of integrative mobile genetic element (IMGE) like prophages, plasmids, transposons or genomic islands, which provides fitness factors that help the pathogen to survive in changing environmental conditions. Metagenomic analyses of clinical and environmental V. cholerae isolates revealed that dimer resolution sites (dif) harbor several structurally and functionally distinct IMGEs. All IMGEs present in the dif region exploit chromosomally encoded tyrosine recombinases, XerC and XerD, for integration. Integration takes place due to site-specific recombination between two specific DNA sequences; chromosomal sequence is called attB and IMGEs sequence is called attP. Different IMGEs present in the attP region have different attP structure but all of them are recognized by XerC and XerD enzymes and mediate either reversible or irreversible integration. Cholera toxin phage (CTXΦ), a lysogenic filamentous phage carrying the cholera toxin genes ctxAB, deserves special attention because it provides V. cholerae the crucial toxin and is always present in the dif region of all epidemic cholera isolates. Therefore, understanding the mechanisms of integration and dissemination of CTXΦ, genetic and ecological factors which support CTXΦ integration as well as production of virion from chromosomally integrated phage genome and interactions of CTXΦ with other genetic elements present in the genomes of V. cholerae is important for learning more about the biology of cholera pathogen.

Oncofertility in adolescent and young adult hereditary cancer: Considerations for genetics professionals

Adolescents and young adults (AYA) with a cancer diagnosis or those at risk for cancer due to hereditary cancer syndromes may benefit from genetic counseling and testing not only to manage personal risk but also to address reproductive concerns, especially fertility. The opportunity for genetic counselors to provide important risk information is relevant to both the newly diagnosed as well as to unaffected carriers and survivors. However, genetic counselors may need additional training in reproductive options related to AYA cancer to provide this valuable counsel. This commentary uses hereditary breast and ovarian cancer syndrome as a model to highlight important considerations when discussing preimplanatation genetic diagnosis and prenatal diagnosis, particularly in the context of expanded testing for hereditary cancer risk including multigene panels or whole exome or whole genome sequencing. Other hereditary cancers are also addressed; however, less is known about the psychosocial and fertility concerns in these AYA populations. Additionally, we provide an overview of the concept of “oncofertility” - the linkage between cancer care and reproductive medicine that aims to expand the reproductive opportunities of cancer patients - and offer support for the expansion of guidelines to include genetic counselors in AYA cancer patients’ treatment planning related to reproductive health and fertility.

Celiac sprue - a cryptic disease: A case report

BACKGROUND

Celiac sprue, or celiac disease, is a relatively common disease whereby many are unaware that they have it. It often manifests with symptoms outside of the digestive system. Many health care providers are unaware of the wide variety of symptoms of celiac disease as well as diseases that are associated with it, often delaying diagnosis and treatment.

CASE SUMMARY

The following case indicates an otherwise healthy 20-year-old female who presents with a variety of symptoms and is ultimately diagnosed with shingles, infectious mononucleosis, and celiac disease

CONCLUSION

Although it is known that risk-factors are genetic as well as environmental, much more research is needed to better understand the relationship of potential causes. In addition, continuing education is needed in health care so that more practitioners better understand celiac disease.

Research progress in the cell origin of basal cell carcinoma

Identification of the cell origin of human neoplasms remains a challenging but important task in cancer research. The outcomes in this area of study may allow us to design novel strategies for early cancer detection and targeted cancer therapeutics. Skin is a great organ to study cancer stem cells because stem cells in skin have been well investigated and approaches of genetic manipulation in specific cell compartments are available to mimic clinical skin cancer in a mouse model. Recently, by using different genetic engineered mouse models, several groups have tried to discover which cell type in skin was responsible for the initiation of basal cell carcinoma, the most common type of skin cancer. These studies raised more questions but also showed more ways for future investigation.

Fiber-fluorescence in situ hybridization analyses as a diagnostic application for orientation of microduplications

Microduplications are normally invisible under microscopy and were not recognized before chromosomal microarray testing was available. Although it is difficult to confirm the orientation of duplicated segments by standard fluorescence in situ hybridization (FISH), our data indicates that fiber-FISH analysis has the potential to reveal the orientation of duplicated and triplicated segments of chromosomes. Recurrent microduplications reciprocal to microdeletions show tandem orientations of the duplicated segments, which is consistent with a non-allelic homologous recombination mechanism. Several random duplications showed tandem configurations and inverted duplications are rare. Further analysis is required to fully elucidate the basic mechanisms underlying such duplications/triplications.

Mosaicism of a novel variant in the ANKRD11 gene in a child with a mild KBG phenotype: A case report

BACKGROUND

KBG syndrome is likely underdiagnosed because of mild and non-specific features in some affected patients especially before the upper permanent central incisors eruption at about the age of 7-8 years. Somatic mosaicisms are usually recognized in the parents only after a typically affected son is diagnosed with KBG syndrome. We describe for the first time the mosaicism of a novel variant in a child with a mild KBG phenotype.

CASE SUMMARY

Our patient presented at 24 mo of age with short stature, hand abnormalities, facial dysmorphism and mild developmental delay. Pituitary hypoplasia and central hypothyroidism were also detected. By next generation sequencing (NGS) analysis we found a novel deletion in the ANKRD11 gene (c.4880_4893del.), that can be classified as likely pathogenic for the syndrome, with the percentage of mutated allele of 36%. We considered this finding as causative of the mild and non-specific phenotype for KBG syndrome in our patient, as previously reported in adults. A heterozygous variant in HESX1 gene, classified as variant of uncertain significance, but suspected of causing pituitary hypoplasia and hormonal deficiency, was also found. The patient started levothyroxine and growth hormone treatment.

CONCLUSION

The increased use of NGS analysis may expand the phenotypic spectrum of KBG syndrome because it allows genetic diagnosis of somatic mosaicisms also in children.

Molecular genetics of gastric adenocarcinoma in clinical practice

The molecular genetics of gastric carcinoma (GC) dictates their biology and clinical behavior. The two morphologically distinct types of gastric carcinoma by Lauren classification, i.e., intestinal and diffuse cell types, have a significant difference in clinical outcome. These two types of GC have different molecular pathogenetic pathways with unique genetic alterations. In addition to environmental and other etiologies, intestinal type GC is associated with Helicobacter pylori (H. pylori) infection and involves a multistep molecular pathway driving the normal epithelium to intestinal metaplasia, dysplasia, and malignant transformation by chromosomal and/or microsatellite instability (MSI), mutation of tumor suppressor genes, and loss of heterozygosity among others. Diffuse type shows no clear causal relationship with H. pylori infection, but is commonly associated with deficiency of cell-cell adhesion due to mutation of the E-cadherin gene (CDH1), and a manifestation of the hereditary gastric cancer syndrome. Thus, detection of CDH1 mutation or loss of expression of E-cadherin may aid in early diagnosis or screening of diffuse type GC. Detection of certain genetic markers, for example, MSI and matrix metalloproteinases, may provide prognostic information, particularly for intestinal type. The common genetic alterations may offer therapeutic targets for treatment of GC. Polymorphisms in Thymidylate synthase to metabolize 5-fluorouracil, glutathione S-transferase for degradation of Cisplatin, and amplification/overexpression of human epidermal growth factor receptor 2 targeted by monoclonal antibody Trastuzumab, are a few examples. P13K/Akt/mTOR pathway, c-Met pathways, epidermal growth factor receptor, insulin-like growth factor receptor, vascular endothelial growth factor receptor fibroblast growth factor receptor, and micro RNAs are several potential therapeutic biomarkers for GC under investigation.

Preimplantation testing: Transition from genetic to genomic diagnosis

Preimplantation genetic testing refers to the procedure to determine the genetic status of embryos formed by in vitro fertilization (IVF) prior to initiating a pregnancy. Traditional genetic methods for preimplantation genetic diagnosis (PGD) examine distinct parts of an individual genome, require the development of a custom assay for every patient family, and are time consuming and inefficient. In the last decade technologies for whole-genome amplification (WGA) from single cells have led to innovative strategies for preimplantation testing. Applications of WGA technology can lead to a universal approach that uses single-nucleotide polymorphisms (SNPs) and mutations across the entire genome for the analysis. Single-cell WGA by multiple displacement amplification has enabled a linkage approach to PGD known as “preimplantation genetic haplotyping”, as well as microarray-based techniques for preimplantation diagnosis. The use of microarrays in preimplantation diagnosis has provided genome-wide testing for gains or losses of single chromosomes (aneuploidies) or chromosomal segments. Properly designed randomized controlled trials are, however, needed to determine whether these new technologies improve IVF outcomes by increasing implantation rates and decreasing miscarriage rates. In genotype analysis of single cells, allele dropout occurs frequently at heterozygous loci. Preimplantation testing of multiple cells biopsied from blastocysts, however, can reduce allele dropout rates and increase the accuracy of genotyping, but it allows less time for PGD. Future development of fast SNP microarrays will enable a universal preimplantation testing for aneuploidies, single-gene disorders and unbalanced translocations within the time frame of an IVF cycle.

Circular RNA: The evolving potential in the disease world

Circular RNAs (circRNAs), a new star of noncoding RNAs, are a group of endogenous RNAs that form a covalently closed circle and occur widely in the mammalian genome. Most circRNAs are conserved throughout species and frequently show stage-specific expression during various stages of tissue development. CircRNAs were a mystery discovery, as they were initially believed to be a product of splicing errors; however, subsequent research has shown that circRNAs can perform various functions and help in the regulation of splicing and transcription, including playing a role as microRNA (miRNA) sponges. With the application of high throughput next-generation technologies, circRNA hotspots were discovered. There are emerging indications that explain the association of circRNAs with human diseases, like cancers, developmental disorders, and inflammation, and circRNAs may be a new potential biomarker for the diagnosis and treatment outcome of various diseases, including cancer. After the discoveries of miRNAs and long noncoding RNAs, circRNAs are now acting as a novel research entity of interest in the field of RNA disease biology. In this review, we aim to focus on major updates on the biogeny and metabolism of circRNAs, along with their possible/established roles in major human diseases.